illumina Dragen TruSight Oncology 500 Analysis Software User Guide

DRAGEN TruSight Oncology 500 Analysis
Software v1.1 on ICA
User Guide
ILLUMINA PROPRIETARY
Document # 200015530 v00
August 2022
For Research Use Only. Not for use in diagnostic procedures.

Dragen TruSight Oncology 500 Analysis Software

DRAGEN TruSight Oncology 500 Analysis Software v1.1 on ICA User Guide
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Document # 200015530 v00
For Research Use Only. Not for use in diagnostic procedures.

Getting Started

You can execute DRAGEN ™TruSight ™  Oncology 500 (TSO 500) Analysis Software v1.1 on Illumina ® Connected Analytics (ICA) v2.
Use the following instructions to configure an analysis run in the ICA interface using graphical mode or command-line interface (CLI). For more information about using ICA, refer to the Illumina Connected Analytics support site page. For more information about running a TSO 500 analysis on ICA, refer to the TruSight Oncology 500 support site page.
Prerequisites
To use ICA to perform interactive data analysis, complete the following prerequisites:

1. Purchase ICA and enable ICA Flow.
2. Upload sequencing data files to an ICA project.
3. Make sure a TSO 500 bundle is available when setting up a project.

Analysis Modes and Configuration

In ICA v2, there are two modes available to launch analysis:

• Graphical user interface
• Command-line interface (CLI)
  When starting a new analysis for DRAGEN TSO 500 Analysis Software v1.1, select a TSO 500 project, TSO 500 pipeline, and the appropriate storage size.
  For DRAGEN TSO 500 Analysis Software v1.1 on ICA v2, storage size depends on the data set. Using the small or medium storage option is usually sufficient. However, S4 flow cells require the large storage option.

Graphical Mode
In graphical mode, the following pipeline run settings must be configured to initiate a DRAGEN TSO 500 Analysis Software v1.1 run successfully.

starting from FASTQ files, this folder is optional.
fastq folder| Folder| No| The path to the FASTQ folder containing FASTQ files. If starting from BCL files, this folder is optional.
resource folder| Folder| Yes| The path to the resource folder.
hashtable folder| Folder| Yes| The path to the hashtable folder.
sample pairids| String| No| A comma-delimited list of pair IDs or sample IDs to process. Use this field to restrict analysis to a subset of pair IDs or sample IDs.
first tileonly| Bool| No| A flag to specify using only the first flow cell tile.
start from_fastq| Bool| No| A flag to specify starting from FASTQ files. This flag must be set to true if fastq_folder is provided. The flag must be set to false if run_folder is provided.

ICA CLI
The same configuration fields as described in Graphical Mode on page 1 must be modified for each ICA  CLI run.
Analysis Methods
The DRAGEN TSO 500 Analysis Software v1.1 uses the following tools to analyze sequencing data.

• DNA Analysis Methods
  – DNA Alignment and Realignment
  – Read Collapsing
  – Indel Realignment and Read Stitching
  – Small Variant Calling
  – Small Variant Filtering
  – Copy Number Variant (CNV) Calling
  – Phased Variant Calling
  – Variant Merging
  – Annotation
  – Tumor Mutational Burden (TMB) Scoring
  – Microsatellite Instability (MSI) Status
  – Contamination Detection

• RNA Analysis Methods
  – Downsampling
  – Read Trimming
  – Alignment
  – Duplicate Marking
  – Fusion Calling
  – RNA Fusion Filtering
  – Splice Variant Calling
  – Annotation
  – Fusion Merging

For more information on analysis methods, refer to DRAGEN TruSight Oncology 500 Analysis Software v1.1 User Guide (Document # 200014849).

Output Folders

This section describes each output folder generated during analysis and where to find metric and analytic files when the pipeline is executed on ICA.
High-Level Folder Structure

Analysis Folder
The analysis folder contains the following two subfolders:

Logs_Intermediates—Contains folders for each submodule in the DRAGEN TSO 500 Analysis Software v1.1 on ICA pipeline. The folders contain a copy of all the relevant files required to create the metric output files and report files, as well as the combined log files at the root level and subfolders for each sample.

| analysis-folder
---|---
| Logs_Intermediates
| AlignCollapser
| Annotation
| Cleanup
| CnvCaller
| CombinedVariantOutput
| Contamination
| DnaFastqValidation
| DnaQCMetrics
| FastqDownsample
| FastqGeneration
| MergedAnnotation
| MetricsOutput
| Msi
| PhasedVariants
| ResourceVerification
| RnaAlignmentFusionCaller
| RnaAnnotation
| RnaFastqValidation
| RnaFusionMerge
| RnaQCMetrics
| RnaSpliceVariantCalling
| RunQc
| SampleAnalysisResults
| SamplesheetValidation
| SmallVariantFilter
| StitchedRealigned
| Tmb
| TrimFastq
| VariantCaller
| VariantMatching

Results—Contains the aggregated MetricsOutput.tsv file and the combined dsdm.json file at the root level. Additionally, the Results folder contains a subfolder for each sample.

| analysis-folder
---|---
| Results
| MetricsOutput.tsv
| sample_1
| sample_2
| dsdm.json

Each sample subfolder contains files required for generating result metrics and the files relevant for analysis.
If using only DNA samples, the Results subfolder contains the following files:

| analysis-folder
---|---
| Results
| MetricsOutput.tsv
| {DNA_Sample_id}
| CombinedVariantOutput.tsv
| CopyNumberVariants.vcf
| DNAMergedSmallVariants_Annotated.json.gz
| MergedSmallVariants.genome.vcf
| MergedSmallVariants.vcf
| TMB_Trace.tsv

If using only RNA samples, the Results subfolder contains the following files:

| analysis-folder
---|---
| Results
| MetricsOutput.tsv
| {RNA_Sample_id}
| AllFusions.csv
| CombinedVariantOutput.tsv
| RNA_Annotated.json.gz
SpliceVariants.vcf

If using only DNA and only RNA samples, the Results subfolder combines both previous structures as follows.

| analysis-folder
---|---
| Results
| MetricsOutput.tsv
| {DNA_Sample_id}
| CombinedVariantOutput.tsv
| CopyNumberVariants.vcf
| DNAMergedSmallVariants_Annotated.json.gz
| MergedSmallVariants.genome.vcf
| MergedSmallVariants.vcf
| TMB_Trace.tsv
| {RNA_Sample_id}
| AllFusions.csv
| CombinedVariantOutput.tsv
| RNA_Annotated.json.gz
| SpliceVariants.vcf

If using paired DNA and RNA samples, the Results subfolder contains the following files::

| analysis-folder
---|---
| Results
| MetricsOutput.tsv
| {Pair_id}
| CombinedVariantOutput.tsv
| {DNA_Sample_id}
| CopyNumberVariants.vcf
| DNAMergedSmallVariants_Annotated.json.gz
| MergedSmallVariants.genome.vcf
| MergedSmallVariants.vcf
| TMB_Trace.tsv
| {RNA_Sample_id}
| AllFusions.csv
---|---
| RNA_Annotated.json.gz
| SpliceVariants.vcf

Cromwell Executions
Cromwell log files are generated from the execution of the DRAGEN TSO 500 Analysis Software v1.1 on ICA pipeline. The files are grouped by the subworkflow and the pipeline task that is being executed.

Revision History

Document #
200015530 v00| August
2022| Initial Release

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For Research Use Only. Not for use in diagnostic procedures.
© 2022 Illumina, Inc. All rights reserved.

References

• Illumina | Sequencing and array solutions to fuel genomic discoveries
• Legal | Legal Information for this website
• TruSight Oncology 500 Support
• Illumina Connected Analytics Support

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